Dear Dr Case,
>> Adding 'set(MINICONDA_VERSION py310_23.5.2-0)' line 91,
>> i.e. forcing the use of python3.10 instead of python3.11, before:
>> set(MINICONDA_INSTALLER_FILENAME "Miniconda${PYTHON_MAJOR_RELEASE}-...
>> in amber22_src/cmake/UseMiniconda.cmake seems to solve the problem.
>
> Have you applied update.3 for AmerTools23? That is supposed to fix the
> problems with python 3.11.
Thank you for your answer.
Yes I checked the patches were applied in the 'cmake.log' before
sending the 2 former emails.
I re-ran the whole process once again; see below...
and I just checked the patches were applied; see below also...
Best Francois
[fyd.login02 ~/bin]$ cd amber22_src/build
[fyd.login02 build]$ egrep 'update\.|Python Interpreter' cmake.log
-- >>> Downloading AmberTools 23/update.1 (1.82 KB)
-- >>> Applying AmberTools 23/update.1
-- >>> Downloading AmberTools 23/update.2 (431.73 KB)
-- >>> Applying AmberTools 23/update.2
-- >>> Downloading AmberTools 23/update.3 (9.18 MB)
-- >>> Applying AmberTools 23/update.3
-- >>> Downloading AmberTools 23/update.4 (20.03 KB)
-- >>> Applying AmberTools 23/update.4
-- >>> Downloading Amber 22/update.1 (1.94 KB)
-- >>> Applying Amber 22/update.1
-- >>> Downloading Amber 22/update.2 (10.78 MB)
-- >>> Applying Amber 22/update.2
-- >>> Downloading Amber 22/update.3 (238.18 KB)
-- >>> Applying Amber 22/update.3
-- >>> Downloading Amber 22/update.4 (3.57 KB)
-- >>> Applying Amber 22/update.4
-- -Python Interpreter: Internal Miniconda (version 3.11)
[fyd.login02 build]$ tail -n 12 install.log
removing: _configtest.c _configtest.o _configtest
building 'mpi4py.MPI' extension
/opt/ohpc/pub/compiler/gcc/9.4.0/bin/gcc -DNDEBUG -fwrapv -O2 -Wall
-fPIC -O2 -isystem
/users/fyd/bin/amber22_src/build/CMakeFiles/miniconda/install/include
-fPIC -O2 -isystem
/users/fyd/bin/amber22_src/build/CMakeFiles/miniconda/install/include
-fPIC -pthread -DPyMPI_MISSING_MPI_LB=1 -DPyMPI_MISSING_MPI_UB=1
-DHAVE_DLFCN_H=1 -DHAVE_DLOPEN=1
-I/users/fyd/bin/amber22_src/build/CMakeFiles/miniconda/install/include/python3.11 -I/opt/ohpc/pub/mpi/openmpi4-gnu9/4.1.1/include -c src/MPI.c -o
/users/fyd/bin/amber22_src/build/AmberTools/src/mpi4py-3.1.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-cpython-311/src/MPI.o
In file included from src/MPI.c:4:
src/mpi4py.MPI.c:198:12: fatal error: longintrepr.h: No such file or directory
198 | #include "longintrepr.h"
| ^~~~~~~~~~~~~~~
compilation terminated.
error: command '/opt/ohpc/pub/compiler/gcc/9.4.0/bin/gcc' failed with
exit code 1
make[2]: ***
[AmberTools/src/mpi4py-3.1.3/CMakeFiles/mpi4py.dir/build.make:203:
AmberTools/src/mpi4py-3.1.3/CMakeFiles/mpi4py-build/mpi4py-build.stamp] Error
1
make[1]: *** [CMakeFiles/Makefile2:3534:
AmberTools/src/mpi4py-3.1.3/CMakeFiles/mpi4py.dir/all] Error 2
make: *** [Makefile:156: all] Error 2
[fyd.login02 ~/compil]$ diff
amber22_src/AmberTools/src/pytraj/pytraj/analysis/c_action/actionlist.cpp
amber22_src.origin/AmberTools/src/pytraj/pytraj/analysis/c_action/actionlist.cpp
1c1
< /* Generated by Cython 0.29.35 */
---
> /* Generated by Cython 0.29.25 */
26,27c26,27
< #define CYTHON_ABI "0_29_35"
< #define CYTHON_HEX_VERSION 0x001D23F0
---
> #define CYTHON_ABI "0_29_25"
> #define CYTHON_HEX_VERSION 0x001D19F0
[...]
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Received on Fri Jul 14 2023 - 19:30:02 PDT
